Bardhan Jaydeep P, Knepley Matthew G
Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, USA.
Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA.
J Chem Phys. 2014 Oct 7;141(13):131103. doi: 10.1063/1.4897324.
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405-2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.
我们表明，在用一个简单的非线性边界条件取代标准电位移边界条件后，使用线性泊松理论可以准确地模拟电荷符号依赖的不对称水合作用。通过使用单个乘法缩放因子从分子动力学 Lennard-Jones 参数确定原子半径，新模型准确地再现了以下物质水合不对称性的分子动力学自由能计算结果：(i) 单原子离子，(ii) 处于质子化和非质子化状态的可滴定氨基酸，以及 (iii) Mobley“手镯”和“棒”测试问题 [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405 - 2414 (2008)]。值得注意的是，该模型还证明了使用线性响应表达式来计算充电自由能的合理性。我们的边界元方法实现展示了其他连续介质静电求解器可以多么容易地扩展以纳入不对称性。
